• Synechococcus Nägeli, 1849
• Synechococcus aeruginosus Nägeli, 1849 accepted as Cyanothece aeruginosa (Nägeli) Komárek, 1976
• Synechococcus ambiguus Skuja, 1937
• Synechococcus amethystinus J.J. Copeland
• Synechococcus amphigranulatus (Copeland) Yoneda, 1943 accepted as Synechococcus bigranulatus Skuja, 1933
• Synechococcus arcuatus
• Synechococcus bacillaris Butcher, 1952 accepted as Cyanobium bacillare (Butcher) J. Komárek, J. Kopecký & V. Cepák, 1999
• Synechococcus bigranulatus Skuja, 1933
• Synechococcus bosshardii Skuja
• Synechococcus brunneolus Rabenhorst, 1863
• Synechococcus caldarius Okada, 1939
• Synechococcus capitatus A.E. Bailey-Watts & J. Komárek, 1991
• Synechococcus carcerarius R.E. Norris, 1967
• Synechococcus cedrorum Sauvageau, 1892 accepted as Cyanobacterium cedrorum (Sauvageau) Komárek, Kopecky & Cepák
• Synechococcus crassus Archer, 1867 accepted as Cyanothece aeruginosa (Nägeli) Komárek, 1976
• Synechococcus curtus Setchell, 1907 accepted as Rhabdoderma curtum (Setchell) Komárek & Anagnostidis, 1995
• Synechococcus diachloros Skuja, 1939 accepted as Cyanobacterium diachloros (Skuja) J. Komárek, J. Kopecký & V. Cepák
• Synechococcus diatomicola Geitler, 1953 accepted as Cyanobium diatomicola (Geitler) J. Komárek, J. Kopecký & V. Cepák, 1999
• Synechococcus elongatus (Nägeli) Nägeli, 1849
• Synechococcus endobioticus Elenkin & Hollerbach, 1923 accepted as Synechocystis endobiotica (Elenkin & Hollerbach) Elenkin, 1938
• Synechococcus endogloeicus F. Hindák, 1995
• Synechococcus endophyticus (W. West & G.S. West) Joosten
• Synechococcus epigloeicus F. Hindák, 1995
• Synechococcus euryphyes Beck-Mannagetta, 1926 accepted as Synechocystis sallensis Skuja, 1929
• Synechococcus eximius J.J. Copeland
• Synechococcus ferrunginosus Wawrik, 1979
• Synechococcus fuscus Zeller, 1873 accepted as Cyanothece aeruginosa (Nägeli) Komárek, 1976
• Synechococcus gaarderi Ålvik, 1934 accepted as Cyanobium gaarderi (Ålvik) J. Komárek, J. Kopecký & V. Cepák, 1999
• Synechococcus geitleri De Toni, 1936 accepted as Synechococcus elongatus (Nägeli) Nägeli, 1849
• Synechococcus grandis Playfair, 1918 accepted as Cyanothece aeruginosa (Nägeli) Komárek, 1976
• Synechococcus intermedius Gardner, 1927
• Synechococcus koidzumii Yoneda, 1943
• Synechococcus leopoliensis (Raciborski) Komrek
• Synechococcus linearis (Schmidle & Lauterborn) Komárek, 1970 accepted as Rhabdoderma lineare Schmidle & Lauterborn, 1900
• Synechococcus lividus Copeland, 1936
• Synechococcus major Schröter, 1884 accepted as Cyanothece major (Schröter) Komárek, 1976
• Synechococcus marinus Ercegovic, 1932 accepted as Aphanothece marina (Ercegovic) Komárek & Anagnostidis, 1995
• Synechococcus marinus Jao, 1948
• Synechococcus minervae J.J. Copeland
• Synechococcus minutissimus Negoro, 1944
• Synechococcus minutus W. West, 1912 accepted as Cyanobium parvum (Migula) J. Komárek, J. Kopeck & V. Cepák, 1999
• Synechococcus mucicolus Joosten, 2006
• Synechococcus mundulus Skuja, 1964
• Synechococcus nidulans (Pringsheim) Komárek, 1970
• Synechococcus notatus Skuja, 1964 accepted as Cyanobacterium notatum (Skuja) J. Komárek, J. Kopecký & V. Cepák, 1999
• Synechococcus oceanicus W.T. Hall & G. Claus
• Synechococcus parvulus Nägeli, 1948 accepted as Synechococcus elongatus (Nägeli) Nägeli, 1849
• Synechococcus parvus Migula, 1906 accepted as Cyanobium parvum (Migula) J. Komárek, J. Kopeck & V. Cepák, 1999
• Synechococcus phage P60
• Synechococcus phage syn5
• Synechococcus plancticus G. Drews, H. Prauser & D. Uhlmann, 1961 accepted as Cyanobium plancticum (G. Drews, H. Prauser & D. Uhlmann) J. Komárek, J. Kopecký & V. Cepák, 1999
• Synechococcus praelongus Emoto & Yoneda
• Synechococcus racemosus Wolle, 1881 accepted as Synechococcus elongatus (Nägeli) Nägeli, 1849
• Synechococcus rayssae Dor, 1967
• Synechococcus rhodobaktron Komárek & Anagnostidis, 1995
• Synechococcus roseopersicinus Grunow, 1863
• Synechococcus roseopurpureus G.S. West, 1899
• Synechococcus roseus J.J. Copeland
• Synechococcus rubescens T.P. Chang, 1980 accepted as Cyanobium rubescens (T.P. Chang) J. Komárek, J. Kopeck & V. Cepák, 1999
• Synechococcus salinarum Komárek, 1956
• Synechococcus salinus Frémy, 1941
• Synechococcus sciophilus Skuja, 1964
• Synechococcus sigmoideus (Moore & Carter) Komárek, 1970
• Synechococcus spongiarum Usher et al., 2004
• Synechococcus sublividus Emoto & Yoneda
• Synechococcus subsalsus Skuja, 1939
• Synechococcus sulphuricus Dor, 1967
• Synechococcus vantieghemii (Pringsheim) Bourrelly, 1970
• Synechococcus vescus Copeland
• Synechococcus violaceus Grunow, 1868
• Synechococcus virga-rosea T.P. Chang, 1980 accepted as Cyanobium virga-rosea (T.P. Chang) J. Komárek, J. Kopecký & V. Cepák, 1999
• Synechococcus viridissimus Copeland, 1936
• Synechococcus vulcanus Copeland, 1934